


Flight and Fight (slow updates)

by Winterm



Category: Doctor Who (2005)
Genre: Angst, Cause They Have Not Watched The Episodes Mentioned In A While, F/F, In Which The Author Most Likely Forgets Plotpoints, Kovarian’s not dead, Mind Control, Order Of The Silence, Post-Library River Song, angst with a semi-happy ending
Language: English
Status: In-Progress
Published: 2019-08-05
Updated: 2020-07-28
Packaged: 2020-07-31 21:54:12
Rating: Teen And Up Audiences
Warnings: No Archive Warnings Apply
Chapters: 7
Words: 8,809
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/20122270
Author URL: https://archiveofourown.org/users/Winterm/pseuds/Winterm
Summary: Madame Kovarian —not dead— knows The Doctor must be restrained. She releases River’s consciousness out of the database, programming it into a new mechanical form. This is the bait to lead The Doctor there, along with some tricks of Kovarian’s own, just to make sure any escape will lead to the destruction of them both.





	1. Pilot

**Author's Note:**

> This is actually my very first work here. I previously wrote fanfictions on Google Docs and shared them with friends. This is one of those (unfinished as of now), that I started a few months ago, planned it all out, and never got around to finishing it. Hopefully I have enough motivation to get to the end here. If anyone finds this work in the great depths of others like it, heyo. Comments and Kudos are appreciated if you have constructive criticism or like it enough to hit the Kudos button.

It was weird sometimes, how things work out. In one moment, she was running through the tunnels in the database, enjoying the false adrenaline flowing through her. Then, a sucking feeling. Like someone was grabbing her soul and pulling it out. She could feel CAL move and shift, desperately trying to grab onto her again.  
Then, darkness. She didn’t know if her eyes were open, or she couldn’t see. A clicking noise echoed through her head, and her vision swirled. She could see fuzzy blobs moving around her.  
“Professor River Song.” a voice mused somewhere over her head.  
“Where am I?” It took a while for her vocal chords to reactivate.  
“That’s not important right now.”  
She heard at least three sets of footsteps moving around. She tried to sit up, but her limbs refused to move. If she had any limbs. She couldn’t feel anything.  
“Tell Kovarian she’s rebooted.” the mystery voice said to another set of mystery footsteps.  
“Kovarian?” She could feel her arms now, and thrust them under her to sit up. “How is she here? Why is she here?” She couldn’t hear anyone around her anymore, and she hit her palm against the floor to make sure her hearing was still intact.  
Her vision focused a bit more. She was in a clinically-white room, with wires criss-crossing the wall. A desk and filing cabinet were pushed into the corner. Other than that, it was empty.  
River looked down at her hands. They looked familiar, but only the surface seemed to have any body heat. Under her skin felt deathly cold. And she could see no tendons on the underside of her wrist. Interesting.  
The door swung open and she whipped her head around. “Madame Kovarian.” she spat, loathing in her gaze.  
“Hello, Melody. Or Professor River Song, as you are known to others now.” the other woman said evenly, standing over River. “I see our attempt at bringing you out of the database has been successful.”  
“What was successful? The fact that I am a machine now?”  
“Oh. I see that you have figured out your... current android form.”  
“How else would I get out of that god-forsaken database? A genie? And your attempt at artificial body heat is lacking. I’m not stupid.” she snorted.  
“Of course you aren’t, darling. But it’s good enough.”  
“For what?” asked River, edging away from Kovarian as she tried to pat her (surprisingly realistic) curls.  
“For your husband.” Kovarian said unapologetically. “In case you had forgotten your dear Doctor?”  
River’s eyes widened. “You can’t just ask me to kill him again. It’s not like I would ever do it.”  
“We don’t want him dead, Melody. Just… restricted. We still don’t trust him, you see.”  
River laughed dryly. “He sacrificed himself rather than release Gallifrey from its pocket universe, and you still don’t trust him?”  
“No.”  
“I’m not helping you ‘restrict him.’ Whatever that means.”  
“Well, that’s not really your choice.”  
River raised her eyebrow. “You are going to send me out there and force me to do stuff for you?”  
“No, that didn’t work before. We are just going to keep you here at bait. We’ll see how long it takes him to come here, so we can arrest him. Or we could kill him. One of the two.”  
River stood up, a jolt of energy running through her legs. She grabbed Kovarian by the neck. “You will do nothing of the sort.” She growled as Kovarian smirked. Then she heard the pounding footsteps, with a finger at her neck as she shut down.

…………………………….

A small blue box, the size of a walk-in closet, yet also entire dimension, kept vigilant guard over Her Thief and the New Odd Ones. Everything was quiet, and they hung peacefully in the Time Vortex with no place that they urgently needed to be. That’s when she heard the noise, and the mechanics of her heart leaped in her chest.

……………………………….

The Doctor turned towards her companions, grin on her face. “We’ve rested up quite a bit, yeah? Where should we go next?”  
Yasmin Khan pursed her lips thoughtfully. “I think it’s Ryan’s turn to choose.”  
“Wha’?” Ryan Sinclair, obviously deep in thought.  
“It’s your turn to choose, mate. Stop looking at me like that.”  
“Like what?”  
The Doctor shook her head. She’d never understand humans, the whole brilliant fascinating lot of them. But she still loved traveling with them.  
Out of the blue, a sharp agonizing pain raced through her head. She gritted her teeth and pressed her fingers to her temples.  
“You okay, Doc?” asked Graham O’Brien worriedly. She plastered on a fake smile.  
“Yeah, I’m fine.” She looked up at the ceiling. “The TARDIS called for help.”  
Graham glanced around. “It can do that?”  
“SHE’S alive, Graham. And of course she can.” She spun around and pressed her hand to one of the crystal beams. “What’s got you worked up, girl?”  
The TARDIS gave a shudder and the lights pulsed red for a second. Yaz put a hand in The Doctor’s shoulder, and she flinched.  
“Come on, team. The Old Girl needs us, sometime and somewhere.”  
The ship gave a shudder and raced across the universe, the doors swinging open on their own. The group stepped out cautiously.  
An expansive and featureless building stretched in either direction, gleaming in the bright turquoise sunlight. The Doctor shielded her eyes against the glare.  
“What is it?” asked Ryan, squinting at The Doctor.  
She shivered. The shininess had a hostile coldness to it. “A military base.”  
“Is that why it’s so shiny? Defense?” Yaz pointed out.  
“Yes! Ten points to Yaz!” The Doctor paused and pointed her sonic at the ground and holding it up to her face. “That’s weird.”  
Ryan looked at the sonic, not sure what she was able to get from looking at the crystal embedded there. “What?”  
“This planet isn’t charted. It isn’t on any maps in the universe. An uncharted, unnamed planet. Practically nonexistent.”  
Graham rolled his eyes. “Let me guess. You’re gonna go in that building.”  
The Doctor had already started towards the high metallic walls. She was about halfway there when a wall opened up and a shadowed figure walked out.  
“Which one of you is The Doctor?”  
The Doctor stepped in front of her companions. “I am The Doctor. Exactly who wants to know?”  
The creature stood in front of her for several seconds before replying. “The Order Of The Silence.”

………………………………..

River awoke in a dark room, different than the strange clinic she woke up in. There were no visible doors or windows. She scanned the surrounding area cautiously. It was completely bare. She doubted she could find a speck of dust in here.  
Her first thought was of starving to death, before remembering how she most likely no longer needed to consume food. So, solitary confinement, then. She could wait.

………………………………..

“Yaz, Ryan, Graham, go back to the TARDIS.” The Doctor said urgently.  
Graham crossed his arms. “No way, Doc.” Ryan and Yaz nodded.  
“I need you to get the TARDIS out of here, understand?” The Doctor hissed. “Just go!”  
The creature held up his hand, his whole face face dissolving and reforming as he did so. “No. They stay to bear witness.”  
“Witness what?”  
The being stayed silent, cold eyes penetrating The Doctor’s soul. “We have someone of yours to ensure you behave.” he said quietly. “We have the one we need.”  
“Who?” The Doctor’s voice struggled to remain even, but it trembled a little at the word. “Tell me.”  
“The criminal.” The creature replied in a singing tone. “A time traveler like you. One who stole the hearts of the Time Lord Victorious.” The last word dripped with contempt and loathing.  
“I wasn’t really in my right mind when— wait. How could you—?”  
“Come with us.” The creature said, holding out his hand. This was definitely a trap. Especially because the Silence were behind this set-up. But it was her one chance to find out what was going on. She pressed her fingers to his palm, and reality faded for a moment.

………………………………..

Yaz had gotten used to things like this. But that didn’t mean she liked it any more than she used to. When The Doctor gave her consent to be brought…. well... who knows where they were, all of Team TARDIS had gone as well.  
They appeared in an elegant corridor with plush carpet running the length of the floor. A few people wandered around, carrying tablets and clipboards as they hurried to various destinations. A few creatures like the one who took them there towered above the humans— or human-like— beings. And others, but why couldn’t she remember them?  
The creature’s face melted again and formed into a hard cone with teeth as they waited in a small room off to the side of the hallway. It held up a hand for them to stop. Several minutes went by before a woman in dark clothes, impressive heels, and some kind of eye-patch walked over to them. Yaz could feel The Doctor tense in recognition at the sight of her.  
“Madame Kovarian. To what do I owe this pleasure?” The Doctor drawled icily, eyes narrowing at the lady.  
“Doctor. I see you are on your fifteenth.” The woman replied in the same tone. “Impressive how one could burn through regenerations so quickly.”  
“Why did you want me to come here?” The Doctor said, ignoring her last statement.  
“Because a power such as yourself needs to be contained.” Kovarian answered. “You served the Silence well on Trenzalore. I’m not saying that we do not trust you, Doctor. But... we really don’t.”  
“How kind of you.” The Doctor said sarcastically. “So are you going to give me a quick death this time?”  
“We would offer you an easy and comfortable life here, Doctor. Within our sight, so you could not be… compromised. You would have your friends with you. You could even work in our science department, if you wanted.”  
The Doctor took a few steps back before stopping. “Wait. You said- Well, he said- you have River?”  
Yaz watched the exchange warily. She wasn’t entirely sure what was going on, but she hoped whoever this Madame Kovarian was would let them leave soon.  
“Yes. We do. Another one of the perks to staying here, with us. You see, the Silence are not a bad organization. We realized that killing you was not a good answer to achieving our goal.”  
“And kidnapping and raising a child to be a psychopath was?”  
“I told you, we… rethought our methods. And it isn’t really your choice. We could just as easily keep you here by force.”  
“Yeah, I’m not really one for settling down, me.” The Doctor wrinkled her nose. “So I really have to go. I would forgive you, but pretending to have River Song with you is another obstacle of trust you set up.”  
“But we do, Doctor. Would seeing her give you a change of hearts? Madame Kovarian turned and nodded at one of the spindly creatures Yaz kept forgetting about. “Because that could easily be arranged.”

………………………………..

The Doctor was insanely nervous. For the first time, she hoped River wasn’t there. The Silence were prone to mental torture, which would be awful for River, given that they raised her. The very existence of this building would break her wife’s hearts.  
There was the sharp noise of the transmat system, and a familiar face stood in front of her, looking confused and… was that fear?  
Kovarian turned towards The Doctor with a smug smile. “We took the privilege of taking her from the Library.”  
The Doctor’s hearts leapt to her throat, and she kept telling herself that this was a trick, a mental manipulation to bend her to the Silence’s will. But another part of her was screaming because that was RIVER standing in front of her, ten feet away and looking right at her with those mesmerizing green eyes, her wife had been returned to her at last!  
River looked at The Doctor, Graham, Ryan, and Yaz, slow and calculating, before taking in The Doctor’s clothes. She nodded slightly and looked up on The Doctor, setting her jaw. “Doctor! It’s a trick!” River said. She flinched away from Madame Kovarian, whose face betrayed nothing. “I’m not really- you know- me.”  
The Doctor walked forward and brushed River’s hand. “Feels like you.” she murmured. “How did you know it was me? And if you’re not her, what are you?”  
River’s gaze flicked downward. “I… can’t tell you that.” She didn’t pull away, but hesitated. “It’s…”  
“River.” The Doctor whispered. “Are they threatening you, or me?”  
“I can’t say they are threatening anyone.”  
“So, yes. And probably me.”  
“I... will neither confirm or deny.”  
The Doctor turned to face Kovarian. “Definitely River.”  
River looked panicked. “Doctor—”  
“Hush, Sweetie.” The Doctor paced forward so she was standing right in front of Kovarian, glowering. “How did you do it?” She asked rather forcefully, feeling a rush of irritation at her unfortunate height.  
“Get her out of the Database? Use your brain, Doctor. You must have thought of several ways to do it since she died.”  
“But she’s... her.”  
Kovarian nodded as River shook her head. “Doctor…” she looked sideways at Kovarian. “She needs to know. She will find out sooner or later.”  
The Doctor looked between them. “Know what? What are you not telling me?” her hearts were pounding. If it was River… could it really be River?  
“If you want to use her to get me to stay here and do whatever your organization wants me to do, you better tell me. Now.”  
“Demands will get you nowhere.” Kovarian said coolly. “We don’t need your consent to keep you here, Doctor.”  
The Doctor’s face hardened. “But can you keep me here for long?”  
“Doc,” Graham whispered. “Who is this River?”  
“My wife, if that really is her. And, an organization I DO NOT LIKE VERY MUCH are using her as a BARGAINING CHIP, which means all of them can gladly GO TO HELL.” The Doctor glared at Kovarian, gaze piercing her with absolute loathing.  
“You’re married?” Yaz asked, looking at The Doctor, then quickly away.  
“Is this really the time, Yaz?” The Doctor shot over her shoulder, obviously stressed. “Okay, listen, Kovarian. Give me answers if you know what’s best for you. God, I wish you died the first time.”  
“Doctor. I’m fine. And not me, but I can’t tell you how I’m here.” River cut in.  
“I don’t even know if I’m really here.”  
The Doctor bit her lip. Several minutes ticked by, the group exchanging glances, The Doctor thinking. “Fine,” she sighed in defeat. “I’ll stay here and be good. But the humans go back to Earth, understand?”  
“No!” River cried out. The agony on her face broke The Doctor’s hearts. That look made her want to both run to her wife’s side and torch whoever was responsible to ash. It was very confusing, actually.  
“Sorry, Sweetie.” The Doctor whispered under her breath.  
“Of course we’ll send your ‘Companions’ home.” Kovarian said curtly. “It will be attended to momentarily. I assume you want to say goodbye.”  
“Doc, don’t just send us back.” Ryan cut in. “You can’t just stay here!”  
“On the contrary, I can.” The Doctor replied. “So, goodbye, yeah? I had a good time with you guys. Thanks for being my new best friends.”  
“Well what do we do now? After seeing all that stuff, I mean. It’ll be hard to just go back to a normal life on Earth.” Yaz said stubbornly.  
“And how much of Earth have you seen, Yaz? Travel the world together. Spend time with your family. You’ll never know when you’re gonna lose them. Like Grace, and Yaz’s granddad.”  
Graham didn’t say anything at first. He just turned around and hugged The Doctor, quick and tight. “This is your chance to be with her again, Doc. To be completely honest I’d the same if it was Grace, and I almost did for that silly projection of her. So watch yourself.”  
The Doctor tensed up, then hugged him back, gesturing to the others. “Come on, Team TARDIS. I’m sorry to be the one to split us up.”  
“You have a plan, don’t you, Doctor?” Yaz asked, coming into their embrace. The Doctor gave a little half smile.  
“I’ll think of one before I go crazy. Don’t worry about me.”  
“Bye, Doctor. Thanks for everything.” Graham’s voice was gruff and hinted at sadness, and The Doctor’s hearts pinched.  
“Goodbye, team. A billion points to you all.”  
The Doctor watched her friends walk out the door sadly. It was better this way. At least they would all be safe now.


	2. Everyone Has Plans

**Notes for the Chapter:**

> I had nothing going on today, so I finished this chapter very quickly. I highly doubt the others will come out at this pace. Thanks for any kudos and the lovely comments I got on the last chapter! If there’s any grammar mistakes or typos in this chapter, feel free to tell me. Chapter three should be out sometime in the next week, so stay tuned! Kudos are always appreciated in the form of a ball of warmth in my insides, and comments will be replied to unless I drop dead out of nowhere.

River watched a The Doctor with narrowed eyes and clenched teeth. This wasn’t the first time she had done something stupid, but this time, the stakes were higher than ever. Not that she wasn’t happy to see her wife, (her wife, she could get used to that,) but not like this.

“Are you happy now?” The Doctor asked, glaring intensely at Kovarian. 

“Very,” Kovarian said flatly. She nodded at one of the Silents who were lurking by the door. “They probably would want some time alone.” She had a teasing tone when she smirked over her shoulder that a The Doctor didn’t like.

“Wait.” The Doctor called after her retreating back. “Let River leave too. She doesn’t deserve to stay here.”

“No thanks.” River deadpanned. “And don’t say anything, I’m still mad at you.” She saw The Doctor’s fists clench slightly as she looked back at River.

“We’ll talk about this later.”

“Kovarian left, you know. Now is as good as ever.”

“You’re an android, aren’t you.” River had seen this coming, but she hadn’t expected it to hurt this much.

“Yeah.” River answered. “They downloaded my consciousness into this junk.” She tried to laugh, but it fell short. The two of them fell silent for several moments. “Is… is that okay?”

The Doctor smiled a bit. “Is is okay that I’m a woman now?”

Instead of answering, River wrapped her arms around The Doctor’s waist, giving her a kiss that seemed to stretch for several eternities. 

“I thought you were mad at me.” The Doctor said, flushed.

“I’m very mad at you.” River said. “I know that you would’ve been able to escape if you weren’t such a sentimental idiot.” 

“Sorry.” The Doctor muttered. “Well, why didn’t you want to leave? Spite, or a bit sentimental yourself?”

“I hate you.”

“No you don’t.” The Doctor grinned. “And I doubt they can keep me here. Gallifrey can, in fact, still tamper with this universe. Where have they been?” 

“Plotting this, I presume.” River mused. “Taking me out of the database.”

“I missed you.” The Doctor said. “I kept thinking of ways I could get you out of there, but I was scared of losing you completely.” She hugged River tightly before pulling away with a frown. “I knew I used to be taller.”

River snorted and hugged her back, murmuring in her ear. “As happy as I am to see you, Sweetie, we need to get you out of here.”

“I need to get them to trust me first.” The Doctor’s muffled voice replied. “Also, I won’t deny I do want to spend some time with you before we go on the run.”

River exhaled sadly. “As do I, but at what cost?” 

“Do I look like I care right now?” The Doctor asked, pulling away. “I just lost my best friends and my freedom. The best thing that happened today was finding you.”

“Well, you found me. What can we do to make this day better? Planning your great escape? Killing Kovarian?”

“I wish.” The Doctor laughed. “But I think I need to stay on their good side for now. But I’d totally kill her. And that’s me talking.”

The door opened. “Are you done being weird?” asked a short girl, carrying a clipboard and wearing a too-big lab coat and chunky glasses. “I mean, it doesn’t really matter, because The Doctor needs a health check right now whether she wants to or not.” 

“A health check?” asked The Doctor. “Why would I need a health check?”

“Just protocol. This way, please.” The girl opened the door and waited, and she gave River a small smile. 

“Be back soon. Hopefully.” She gave the girl a look of distrust and followed her back to the main lobby. 

“Over here.” The girl said, opening up a door. The Doctor was watching her surroundings carefully, trying to remember where the entrance door was.

They entered a side hallway and were greeted with a blast of freezing air. The walls were painted a light blue, and the ceiling and floor tiles complimented it with a blinding white. More doors spanned the length of the hall, with names on them in a language The Doctor didn’t know and the TARDIS didn’t translate for her.

“Bring her here, Alice,” said a tall man with dreadlocks, appearing in one of the doorways. Alice led them inside and The Doctor sat down.

“Enjoying your stay so far?” the new man asked her, running his hands through a fine mist conjured in front of them. He gestured for her to do the same. The Doctor stayed silent, unsure of how to answer his question. 

“My name is Michael, and this is my assistant, Alice,” Michael said, turning on his swivel chair to get a clipboard identical to Alice’s.

The Doctor was not in the mood for pleasantries. Being with River was what she got out of the bargain, and they hadn’t even spent ten minutes together yet. “Well, this is a health check, so check me.”

“In a moment, please be patient while I grab some things,” Michael replied. He and Alice stepped out, leaving The Doctor alone in the room. 

With the knowledge that they could come back any second, she crept stealthily over to the desk in an attempt to figure out what was going on. It only took a few seconds to find a map of the building in one of the drawers. The Doctor grinned and had just started to study it when a familiar book snagged her attention. The smile slipped off her face and she hastily pocketed the map and flipped the book open to check the inside cover.

“How did they get River’s diary?” The Doctor murmured to herself as she gently ran her fingers down the spine. The little blue book, a documentation of their travels together, had more information on The Doctor than anything else in the world. Yes, she had to admit she read it once or twice after Darillium, when the loneliness and longing for River caught up to her and made her desperate enough to go back to the Library and take it back. She knew what was in there, and if anyone in the Silence read it, they would know enough to put both of their lives in danger. And it was right there, in their base.

Her thoughts were interrupted by a knock, and she stuffed it into her coat and sat down just before Michael came back into his office. 

“Stand over there, Doctor,” Alice instructed, stepping in after him. Recognizing the equipment they brought as scanners, The Doctor took her coat off before standing in front of them. It was a pitiful and desperate maneuver, as her theft would only be hidden as long as it took them to discover the book and map were missing. 

She had barely enough time to collect her thoughts before Alice hit a button on the wall, almost blinding her.

“Eyugh,” The Doctor groaned as bright red lights turned on and began beaming over her. They scanned her up and down as Alice and Michael scribbled on their twin clipboards. 

The Doctor squinted at the lights, noticing tiny wiggling particles in the beams. They moved towards her and writhed over her skin, giving her an uncomfortable itching sensation. The Doctor felt a tiny prick on her forearm and saw one sink into the veins in her wrist.

“What are you doing?” The Doctor called to Michael, who reached over and turned the red lights off without acknowledging the question. “That was a tracker, wasn’t it?” 

“Yep, just a precaution,” Alice answered for him. “We wouldn’t want anything to happen to you, would we?”

The Doctor scowled and rubbed her hand over her wrist. “Can I go now?”

“Do you need help getting back?” Michael asked, opening the doors for her. 

“I’ll be able to find my way by myself, thanks.”

“Do you want to know the results of the scan? I can get it for you.”

“No thank you,” The Doctor snapped at them. She left and walked back to the room she left River in, rubbing her hand over the diary in the pocket. Who cared about building trust anymore. It was vital that they left, as soon as they possibly could. She just needed to get rid of the tracker and form an escape plan.

………………………………..

The Doctor was visibly upset when she came back in, and River was on her feet in a heartbeat. “What the hell happened in there, Doctor? They said—” she stopped. “Well, Kovarian came back in and wouldn’t tell me what was happening, only that you were ‘taken care of,’ and that we ‘didn't need to worry about escape anymore.’”

The entire conversation with them was a blur, as they kept on shutting her down whenever she tried to strangle Kovarian, which admittedly happened several times. She was still a bit disoriented from that.

The Doctor held up a blue notebook, a pained expression on her face. “They had your diary. For who knows how long before I found it.”

River felt the blood draining from her face. “O-oh.” She reaches to grab it, hand trembling. “That is really, really bad for us. Some of the things in there—”

“I know,” The Doctor said. “I don’t know how they got it, either.” 

River pursed her lips. “Hopefully, they didn’t have it for very long, and…” she trailed off. “Wait, what do you mean, you know?”

“I’m sorry,” The Doctor sighed. “I wasn’t having a very good day, and I missed you…”

River was kind of upset that The Doctor read the diary, but she did think that she was dead, and River was kind of impressed and surprised that her wife waited that long to read it, knowing how curious The Doctor was. “It’s alright, Sweetie. We have bigger issues to deal with. Do you have any ideas on how to get out of here?”

The Doctor pulled a map out of her pocket. “I was given a tracker, but when I get it out I was thinking we could leave through the maintenance tunnel. They shouldn’t be very well monitored, and they lead almost directly to the outside.”

The Doctor and River huddled over the map and continued to make their plans. 

They were unaware of someone else hearing of their schemes through River’s body, and telling her guards to increase their watch on the maintenance tunnels.

**Notes for the Chapter:**

> I tried to make this chapter as fluffy as possible, but there’s a mystery afoot! This chapter was entirely written rewatching the show Good Omens yet again.
> 
> Hey, the last paragraph is pretty confusing now that I reread it. Basically, The Doctor and River are being watched by a strange person that wants to foil their plans.


	3. Villainous Mind Games

**Notes for the Chapter:**

> This is really short, about half as long as the other ones. Sorry, but I have plans for where the chapters start and end and wasn’t able to stretch out my ideas for this as long as I wanted to. There will probably be five or six chapters to this story, but they will get longer from here. Thanks so much for reading!! 
> 
> Very minor gore in this chapter. I’m not even sure if it’s enough to warn about, but I want you to be safe. So, just in case, Be wary of your triggers.
> 
> Please tell me about any typos or if something doesn’t make sense, I’m not the greatest at catching those kinds of things.

It took a few days to refine their plans. No one brought up the missing diary, and everything seemed to be going well enough. They were left alone, for the most part, with workers stopping in around once a day to check up on them. 

They removed the tracker on day two. The Doctor worked on locating it most of the morning, pressing down on her veins to see if she could feel it. Things like that were very delicate from what The Doctor had seen of them, and would usually give some kind of sign once you exploded them.

She found it on the underside of her knee, by the green liquid exploding through the vein there and turning the immediate area green. She winced from that pain and braced herself for more, taking a piece of glass that she sterilized as much as she could to slice open the skin there. 

Neon blood poured from the affected area, and once it started seeping out in a normal color she healed it with regeneration energy. She couldn’t risk an injury in their escape to slow them down, even if that cost her fingernails or something further down the road.

The Doctor left the room they were residing in once to investigate the tunnel. The grate was padlocked shut, but was rusted through and easy to break even without her sonic. Like she expected, there was no one in the tunnel, and she hadn’t run into any guards on the way there either. They should be able to get out easily enough.

The planned day came. They left at night, seeing no one immediately outside their room. The problems began about halfway to the tunnel with one of the Silents, who seemed to know their location. As it turned on them, River shot it in the chest with a gun she had nicked from an officer. There was a search for it, but they were deemed innocent after no evidence was found that she took it.

A small buzz from the gun rang out. It most likely wasn’t loud enough to bring attention to their spot, but they moved quickly away anyway. The maintenance tunnel was within sight.

………………………………..

“Stop,” Kovarian said to the soldiers that went quietly towards the two women. “I want to see what they’ll do.” She had a good handle on the situation. Even if they were able to leave, they wouldn't be able to enjoy their freedom for long. 

Kovarian herself was in control of all the pawns in this game, tucked away in safety behind her screens. If she wanted to, she could shut River Song down then and there. She could even make River kill The Doctor, then and there, with that handy little gun of hers.

An oversight on their part. With that big brain The Doctor had, you’d think she would have suspected foul play by now. She was blinded by her happiness of being with River, and that was a beautiful thing.

Beautiful for Kovarian, at least. 

………………………………..

River could hear footsteps up ahead and held up an arm to make sure The Doctor stopped. She tightened the grip on her gun and they both tiptoed to the tunnel, scanning their surroundings cautiously.

A young teen, inexperienced and jumpy, accidentally fired a shot that barely missed The Doctor’s head. The others took that as a signal to fire, and all hell broke loose.

River was shot several times trying to protect The Doctor, and was barely able to register the sparks and frayed wires erupting from her body before she shut down. 

Kovarian got a handle on the situation again by releasing knockout gas into the area before The Doctor got too injured.

She made a mental note to fire that young boy, and separate The Doctor and River for the time being. For all the entertainment that provided, it was clear that her soldiers needed a break and a good lesson in disobedience.

**Notes for the Chapter:**

> If this was a Disney movie, the villain song would be right about here.
> 
> No, I would not like to see Doctor Who as a Disney movie. There are some things that should never be touched by Disney, and DW is one of them, as much as I love me some good old Disney.
> 
> (However, if there was a Doctor Who musical, I’d be DOWN for that. Just think, it could be called the Whosical...!)


	4. Effects

**Notes for the Chapter:**

> Ha, this isn’t the long chapter I expected it to be. I split my plans into two cause I was too lazy to write both of those.
> 
> Trigger warning for gore in this chapter. Be safe, please!
> 
> Will the next chapter be up soon? Maybe. Do I procrastinate too much for my own good? Yes. Did I write a one-shot in the main time I could work on this? Also yes. (Hotel? Trivago)
> 
> As always, comments and kudos are appreciated. And please, please tell me if you find typos, I’m a MESS and terrible at proofreading my work. I can proofread other people’s work, and that makes everyone think I’m a hypocrite for pointing out their grammar mistakes that I make on my own writing.
> 
> Anyway, here’s the new chapter. Enjoy.

It was dark. The Doctor was on a cold, strangely familiar floor. There was a thick diamond wall in front of him… (him? That didn’t seem quite right), with the buzzing of flies somewhere behind. He looked down at her hands. They were wrinkled and calloused, knuckles burst open and bleeding. He turned around and saw the source of the buzzing, a veiled lady behind him. It all came rushing back to the Doctor. He turned and charged at the wall, punching it in a manic frenzy. The Doctor took a conscious look at the wall, still hitting it. There were humanoid forms behind it and he tried to get a closer look, but fell, the exhaustion catching up to him.

He sat up. He heard the chirping of birds above him, for some reason on a park bench now. There was a page in his hand, and the moment he looked down on it, he felt glasses slide down his face. It was then that he realized he was crying, but he couldn’t for the life of him remember why. He tried to read the page, but instead of the words he somehow already expected, it was just names. They were smudged and covered with tears, he read the few that were still legible. Vicki… Jaime…Zoe … Liz…Romana… Leela… suddenly his head spun, and he dropped the page right as the wind picked up. He ran, trying to catch up to it...

Then, another wall. He was still crying. The wall was a shocking white and completely blank, and he hated that wall for… some reason? The word Rose flashed across his skull, and suddenly, there were people around him.

Suddenly, nothing. A strange sensation of falling. A child in a gas mask in front of him. Velvet suits and bowler hats. A long striped scarf. Glittering eyes in dark tunnels of the London Underground. The Doctor’s breath caught as the dizziness and panic overcame him. Her. Someone… 

………………………………..

She awoke with a gasp. She could hear a fast pulsing next to her ear, and she turned towards it, almost smacking her nose on the heartbeat monitor strapped to the side of her bed. So that was the source of the beeping that was driving her mad.

“Careful.” The Doctor heard. There was someone sitting there. If the room stopped spinning, she might be able to find out who it was. 

“It’s Alice. The medical assistant,” the person helpfully commented. Oh. “The boss told me to keep an eye on you. She also apologizes for the knockout gas, which we hear brings unpleasant dreams.”

No kidding, The Doctor thought. She tried to rise into a sitting position, and the vertigo hit her like a truck. It didn’t help that she was on the ceiling. Was she on the wall now? It was hard to tell.

“Doctor?” She heard Alice say. Her voice was strange and doubled over. We’re human voices supposed to do that?

She was underwater. It was dark down there, and she turned to swim to the surface. She almost made it several times, but it just got farther and farther away. Oh! Martha was there. Martha was a smart doctor. She would know what to do, right?

Suddenly, there was a skull on her face. It was old and shriveled, and very gross. However, she could breathe again now.

Yaz was underwater as well. She looked lost, and The Doctor swam over to help her. Her coat was making it hard to swim, but no matter how hard she tried she couldn’t take it off. “YAZ!” She tried to say, but her words escaped in a bubble. She briefly wondered if the bubble would make it to the surface.

She reached Yaz and placed a hand on her shoulder. For some reason, her companion held a knife. The Doctor frowned. Yasmin knew she hated weapons. She tried to question her, but the skull over her face talked for her, and mixed up her words. Yaz didn’t seem to hear her.

The Doctor swam around to face Yasmin, trying to get her attention. At last she looked up, and made eye contact with her. The Doctor waved and gestured for Yaz to follow her, but the girl tightened her grip on the knife and shook her head.

“You cast us out. You left, and you aren’t coming back.” Yaz said mournfully. “Why should I follow you?”

The Doctor couldn’t reply, and gestured again, pointing to the surface. Yaz swam towards The Doctor, who turned around to lead them out. 

Yaz brought her arm back, and The Doctor didn’t know what was happening until the knife was plunged into her chest. She coughed and convulsed, trying to get away from Yasmin, who only stuck it deeper in. The water around them was turning red. Yaz pushed farther, plunging her hand into the now-gaping wound. 

Then Yaz was gone. The knife was in The Doctor’s hands and she panicked, trying to pull it out. She saw the knife handle come out of her skin, still stuck in the gaping hand-sized hole in her chest. The pain was there, but she felt it almost like an out-of-body experience. She was trying to stop the blood then, but knew it was a lost cause. Her hands began to glow, the golden light mixing into the red water. 

She then passed out from the pain she could barely feel.

………………………………..

There was no water when The Doctor woke up. There was no wound, either. Alice was still there, watching with nervous curiosity.

“Are you there now?” Alice asked. “You passed out again. You were completely incoherent when you were awake before.”

The Doctor realized her hands were shaking and she clutched at the blankets to try to make them stop. Ignoring the feeling that she was going to vomit, she gave a thumbs up. 

She felt she was forgetting something. “Where’s River?” She asked, all of her emotions suddenly replaced with panic. 

“River is being repaired,” Alice said calmly. “There were several holes blown in some very important parts of the wiring, but it’s nothing we can’t fix.”

“Why are you still helping us? I would think we would be ‘punished for our disobedience’ or whatever.”

“You are being punished,” Alice said nonchalantly. “We are separating you two for now, and your living conditions will be slightly less comfortable now. You have three strikes ‘til you’re out, in case you’re wondering.”

“Out being…” The Doctor mimed slicing her throat, ignoring the baseball reference.

“Dead, yes,” Alice replied. “Seeing as you can have a steady conversation, I’ll just see if you can walk in a straight line, then we’ll take you to your new living quarters.”

Three strikes and they were out. The Doctor could work with that.

**Notes for the Chapter:**

> Madame Kovarian’s Knockout Gas: Illegal worldwide
> 
> I guess you could compare the side effects of the gas to an LSD trip


	5. It’s finally up, everyone

**Notes for the Chapter:**

> Sorry for the long wait! Some gore in this chapter.
> 
> Comments and kudos are appreciated but definitely not deserved after postponing this for so long.

River saw The Doctor again a few days later. Both of them were a bit battered, but they were determined and ready to try again.

“I think we are missing something,” River prompted, after a quick embrace. “How did they know we would be leaving through maintenance?”

“There might be cameras in our room we missed before. Or maybe I didn’t get the tracker completely out. Or maybe...” The Doctor started, before trailing off.

River searched her wife’s face, trying to read her expression. “What?”

The Doctor smiled unconvincingly. “Never mind, it was just an idea.”

“Hello, lovebirds,” a voice said, somewhere behind them. They spun around to see Kovarian, wearing something that looked like pajamas. Makeup still covered her face, in pristine condition, though the rest of her looked like she had just woken up.

“What do you want?” River hissed. She felt The Doctor’s shoulders tense under her hands.

Kovarian gave a pinched smile. “We mentioned separate quarters for you two, didn’t we?” she said, as River and The Doctor exchanged panicked looks. “Didn’t we?” Kovarian repeated more forcefully, smile dropping from her face.

River felt The Doctor press something into her hand. She concealed it, making a mental note to look at it later.

The Doctor straightened her shoulders and met Kovarian dead in the eye. “Yes, you did.”

“In that case…” Kovarian said again, her voice barely above a murmur, “Say your goodbyes for now.”

The Doctor and River didn’t do anything besides giving each other a firm nod.

“Might I ask,” started The Doctor; “How are you alive?” River laughed internally at the question, it seemed to have bothered The Doctor for a while.

Kovarian frowned. “I suppose it makes no difference,” she mused. “To answer your question, things that happen on a parallel timeline never stay permanent. I wonder what that means for your marriage…”

On that note, she pressed a button on her pajama shirt and two of the shapeshifting servants came to take The Doctor away.

“Come along Melody, dear.” Kovarian said, and began to decend a flight of stairs. There were none of the shapeshifters or Silents to make sure she did, but River realized she had no choice but to follow.

She willed her legs to stop, but they just kept going. Down… down… down… River counted the steps, realizing she really only had control over her thoughts. Her own body had betrayed her, but it was made by the Silence. It really was no surprise.

It reminded her of the astronaut suit, with the same sensation of having no control over her own limbs. The suit would move for her, and later in life it moved in a way she hated.

There was noise up ahead, and River realized they were walking through some kind of commons. Madame Kovarian stopped there, and River came to a halt as well. The room was filled with soldiers, all facing towards the far wall.

Kovarian pushed through them, leaving River where she was. River could only see glimpses of what was going on over the heads of the people. She watched Kovarian grab a silver pistol from a case embedded into a wall, and then she turned to face the crowd. Then she spoke.

“We have a traitor in our midst,” she called to the crowd. The soldiers moved to look at one another, blocking River’s view. River tried to regain control over her body, but she was still frozen.

“Who is the traitor?” Kovarian asked the assembled soldiers, her steely gaze sweeping over them. “It just so happens to be traitorS, plural. Everyone in this room attacked our escaping guests against my orders. If you don’t remember, I told you to WAIT.” On that note, she raised her hand, and several Silents stepped onto the podium. “I waited to do this so that you could watch, River. This way you can see the consequences of your betrayal.”

A few soldiers turned, only just realizing she was there. Several things happened then: None of them were wearing eye drives, and forgetting about the Silents, they let their guard down as they turned. Their mistake.

Kovarian fired the pistol into the air, which seemed to be some sort of signal. The Silents opened their mouths, sucking electricity out of the air. Kovarian looked on as lightning erupted out of their hands, striking the crowd, who were frozen in fear. Their shouts were quickly cut off as they exploded, blood and skin splattering the walls.

It was then that River realized she was in pain. Whatever circuitry was in her felt scrambled and wrong. The newly implanted fake flesh looked burned and torn, most likely hit by the Silents’ careless electricity.

There was another new development. Her arm moved of her own free will. She looked back to Kovarian. She was not looking at River, busy giving instructions to obviously terrified cleaning people to clean up the human remains.

River took the opportunity to run, which she did until she reached a deserted corridor. She popped the ceiling tile and pulled herself up, closing it behind her. In the dim light coming from below, she read the message from The Doctor, which she only just remembered was there.

_I think are cameras in your eyes. Probably trackers as well._

That explained a lot, actually. She wondered when The Doctor had time to write that, and held onto that thought to calm herself as she pulled out her eye. The artificial pain only lasted for a second, and she turned the eye over in her hand to inspect it while she could still see. Within the cut and frayed wires along the back, there was a small camera embedded there.

She destroyed the eye and took out the other one, letting her world plunge into darkness.

**Notes for the Chapter:**

> Only Kovarian can order a mass execution in her pajamas.


	6. The Chapter I Put Off Way Too Long

**Summary for the Chapter:**

> The Doctor’s life has taken a turn for the worse, and it has recently become the most boring thing she has ever had the displeasure to experience. All that changes when she receives both a visitor and news.
> 
> Trigger Warning: Torture

**Notes for the Chapter:**

> Sorry this took so long. I’ve gotten some things sorted out and recently got super involved with this fic, so I quickly wrote a thing to post here. Thank you for the support, I will aim for more regular updates. My sister has not edited most of this thing yet so if you spot anything that needs fixing please tell me.

The cell The Doctor was kept in was a definite downgrade from their old room. The bright fluorescent bulbs both blinded and annoyed her by the buzz of old electricity, and the same lights turned off promptly at 9 pm every night, leaving only a dim glow from the hallway to see where she was going.

The actual room was furnished like a half-finished movie set of a hotel room, with a bed and adjoining bathroom. The half-finished part came from the patchy carpet on only select areas of the floor, and the overall blandness of the room. It seemed to be perfectly engineered to drive The Doctor insane.

That is why she spent most of the first day on the bed, eyes shut tight, trying to form an escape plan. The first one had failed horribly, so she picked at the other half-formed plans they had come up with to find any escape possibilities at all.

She worried for River. Her wife could be anywhere, they might have even switched her off and put her back into storage. She especially missed the old flesh-and-blood version of River. The android with her wife’s soul seemed off and tampered with, which is how The Doctor formed her camera hypothesis in the first place.

Speaking of, she wondered if River ever read her note. She felt bad for telling River to take out her eyes, but without that they would never be able to escape.

The Doctor rolled onto her side and continued thinking about River. They were trapped before, but at least they were together…

She had no idea where River was now. Absolute longing for them to be together made every single bone in her body ache. 

She heard the door creak open and she turned her head to look at what was going on. It was Kovarian, here to do something or another. “What do you want?”

“Hello, Doctor,” Kovarian said coldly. “We have some questions for you.”

“And I have a question for you,” The Doctor hissed. She stalked across the room, feeling some of the old oncoming-storm-energy she got when she was particularly angry. And she was angry. “Where. Is. My. Wife.”

“That is just what we were going to ask you, but it seems you wouldn’t know either.”

The Doctor huffed. She wished she could gather up all of the frustration and anger she felt and use it to throw Kovarian against the wall. Repeatedly. She went with a good old-fashioned punch at her face, and though it did knock her hated opponent back a few feet The Doctor’s triumph was short-lived.

Once Kovarian got her bearings, she hit a small button concealed in her suit pocket. The Doctor screamed as pain rocketed through her veins, boiling her blood and erasing all thoughts except for the pure agony she was in. It was like liquid fire had consumed every cell in her body, kind of like regeneration. But it just kept going.

Seconds passed before Kovarian released the button, but it felt like several eternities. The Doctor’s limbs went limp as if all of her muscles just gave up in that moment. She tried to will herself to move, but the only response to her efforts was a small twitch of her thumb.

Kovarian kneeled next to The Doctor and raised her chin with a cold, sharp finger. “Maybe you have learned from your mistakes, and you won’t try that again. You see, no matter how many times you dig out that little tracker, we will always be able to put another one in. I’d suggest you stop trying and cooperate with us next time we come to visit.”

The Doctor strained to speak, her voice barely a whisper. “Why… don’t you just kill me then ...? It must be a… strain on… resources.” The simple question drained the little energy she had left in her body.

“Oh, you have a lot of protections put on you from various places in the universe, and we would prefer to skip that paperwork. However, we will if pushed, and we are already so close to the edge. Bye-Bye, Doctor. Behave yourself.” Kovarian twisted the black box with the horrid button in her hands, careful that it remain in The Doctor’s line of sight.

The Doctor laid back down on the floor in an attempt to relax. Beads of sweat dripped down her face, and she still was barely able to move. It was in this state that a realization hit The Doctor.

Kovarian didn’t know where River was. River had gotten out.

For the first time since she was brought to that room, The Doctor smiled.

**Notes for the Chapter:**

> This was supposed to be the reunion chapter, so whoops.


	7. Hello Again

**Notes for the Chapter:**

> I’m sorry for how long this took to update. I’m losing motivation to write this, and as I do so the chapters get shorter (and progressively worse) I want to be proud of each update I put out, and I haven’t been a fan of the last few. So here’s the new update, it’s still very short but it gets into what River has been up to this whole time.
> 
> Comments and kudos are appreciated.

In the day or so she has been in the ceiling, River had tried to cope with the sudden blindness. She knew finding The Doctor would be their only hope of escape but it was hard when she could’ve been crawling in circles as far as she knew.

The ceiling itself was suffocatingly hot and smelled strongly of mold. River had almost overheated several times already, with only a tiny whirring fan where her liver would be to help cool her down. That was what was going on now, as River kept moving at her slow and careful pace trying to ignore the vibrating. 

Without the need to eat, sleep, or rest, River knew she would have gained quite a lot of ground unless she was really crawling in circles. It sure felt like it.

After an indefinite amount of time she heard muffled thumping coming from behind her, getting steadily closer. The source of the thumping was muttering into a staticky radio, which couldn’t mean anything good.

River reached out a hand and felt around the wall until she grasped a metal pipe that was near her head. It was rough and almost too cold to touch, but she grasped it firmly and pulled as hard as she could. About a foot of the pipe came loose with a slight pop and then a hiss of air as the contents spilled into the tunnel. The thumping stopped.

She leaned backwards against the wall, desperately hoping she was out of sight. After a few agonizing moments, a shout rang out from down the hall.

Her attacker crawled quickly towards River, and she heard them curse and stumble as they hit their head on the ceiling. River brandished her pipe.

They were on her in a matter of moments. River wasn’t used to fighting blind, but she knew she probably still had the advantage. She twisted and attempted to kick them off of her. They were temporarily dislodged and River swung towards them with the pipe.

Making a dull clanging noise was the only thing the pipe did, and River found the area in which she was fighting was a lot smaller than she thought it was. Her attacker gripped her arm as it struck the wall and pinned the pipe down. 

River needed to think. She curled her other hand into a fist and hoped she was aiming somewhere useful. The impact of her fist made her attacker grunt -a man, she was pretty sure- as it landed in the center of his chest.

Immediately after she grasped the side of the tunnel closest to the man and grinned at her luck. She pulled the pipe-wielding hand away from the soldier man and swiped at the tangle of wires, knowing at least a few had broken by the electrical crackling coming from there. The man readjusted his position and grabbed the pipe, realizing his mistake too late as the electricity consumed the copper tube. He screamed and River pushed the pipe down harder, gritting her teeth as the buzz whipped through her hand. She could feel the artificial skin burning off, and the pain was almost too much to handle. 

A few moments later she heard the man's body fall against the floor and she gladly let the pipe drop. She had no idea what was in those wires, but seeing as it was enough to knock out a full grown adult she wasn’t going to hang around the exposed currents of death much longer.

River had just stopped to catch her ‘breath’ when a woman’s scream sounded in the distance. She lifted her head in triumph, then alarm.

It wasn’t exactly a definite clue, but it was something. And honestly, River would take what she could get. 

Finding out how to get to the source of the noise was a problem. She hit dead ends multiple times and had to backtrack constantly. That’s when the laughing started. It was crazed in nature and kept breaking into coughs. And it was close.

Heart pounding, she squeezed through the tunnel until she was right above the source of the noise and kicked the plaster underneath her as hard as she could.

She landed hard on the cold tile floor and tried to orient herself. The laughing stopped.

“River?”

She smiled happily and turned her head to the noise. “Hello again, sweetie.”

**Notes for the Chapter:**

> That was my first attempt at writing a fighting scene, I hope it went okay.


End file.
